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Biochemistry > Lecture 1 - Human Genome Organization > Flashcards

Lecture 1 - Human Genome Organization Flashcards

1
Q

What does genome refer to?

A

The genetic material in an organism

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2
Q

What does the genome comprise of in eukaryotes?

A
  • comprised of both nuclear + mitochondrial genomes
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3
Q

Describe the following regarding the nuclear genome :

  • Location
  • DNA copies
  • Genome structure
  • Genome size
  • Number of genes
  • Coding region (%)
  • Mode of inheritance
A

Location : Nucleus

DNA copies: 2 copies of 23 chromosomes per cell

Genome Structure: Linear DNA

Genome size: 3.2 x 10^9 base pairs

Number of genes: 30,000

Coding region : 2% ( 98% Non-coding )

Mode of inheritance : Nuclear DNA inherited from both mother & father (diploid)

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4
Q

Describe the following regarding the Mitochondrial genome :

  • Location
  • DNA copies
  • Genome structure
  • Genome size
  • Number of genes
  • Coding region (%)
  • Mode of inheritance
A

Location : Mitochondria

DNA copies : Several copies of mt-DNA (2-10) per mitochondrion. Each cell contains multiple mitochondria, therefore each cell estimated 1,000-10,000 copies of mt-DNA.

Genome structure : Circular DNA

Genome size : 16,569

Number of genes : 37 genes

Coding region (%) : 97 ( 3% non-coding )

Mode of inheritance : Inherited only from mother (Haploid)

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5
Q

Describe what a Genome is :

A
  • Total DNA content in a cell
  • Contains all DNA including protein coding genes
  • Each organism has one genome
  • Study of properties of the genome is known as genomics
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6
Q

Describe what a Gene is :

A
  • Segment of a total DNA molecule
  • Only contain protein coding DNA
  • Thousands of genes present in an organism
  • Study of properties of genes known as genetics
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7
Q

Describe the structure of the human genome:

A
  • Two nucleotides linked together by equal covalent bonds between the sugar of one nucleotide & phosphate group of another.
  • many nucleotides joined together this way to form one strand of DNA
  • DNA molecules consist of two strands of nucleotides wound together into a double helix
  • Hydrogen bonds link the two strands together
  • Complementary base pairing ( A-T & C-G ) occurs between the two strands
  • The two strands run anti parallel ( 5’ to 3’ on one stand & 3’ to 5’ on the other )
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8
Q

What is Chargaff’s rule?

A
  • A (30.9%) = T (29.4%)
  • C (19.8%) = G (19.9%)
  • Purines = Pyrimidines
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9
Q

What is the size of the DNA per cell? And what can it be divided into?

A
  • 2 meters of DNA
  • 46 human chromosomes
  • 3 billion subunits/base pairs
  • Approx 30,000 genes
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10
Q

How are such large DNA fibres compactly packaged in a small nucleus?

A
  • Linear chromatin (DNA) fibres are tightly packed with Histone (H2A, H2B, H3 & H4) proteins.
  • Dimers of histone proteins first form an octamer protein complex.
  • The octamers bind & wrap the DNA around twice
  • Each complex of Histone proteins & DNA wrapping around them is called nucleosomes
  • Nucleosomes are separated by a 30-bp linker DNA
  • Histone H1 binds on the linker site & protects the nucleosomes from becoming a mess/tangle
  • All the nucleosomes condense further to form a loop like structure
  • This loop structure further coils & gets denser to form a sister chromatid as seen in metaphase.
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11
Q

What occurs during the mitosis cell division & in which phase precisely?

A
  • Metaphase stage
  • Linear DNA packing w/ histone proteins
  • Formation of a supercoiled sister chromatid
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12
Q

What is the significance of the Metaphase Chromosomes? Give an example.

A
  • Used in karyotyping
  • to identify chromosome number & structural abnormalities
  • XO, XXY which is translocation error
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13
Q

Describe the Denaturation of the DNA double helix :

A
  • When a double stranded DNA in solution is heated, the H-bonds holding the two strands together start breaking
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14
Q

At what temp. does denaturation occur? What does the particular temp. depend on?

A
  • Denaturation of DNA at a particular temp depends on G-C & A-T content of DNA
  • DNA containing A-T base pairs melts @ 70C due to weaker 2H bonds
  • DNA containing G-C base pairs melts @ over 95C due to stronger 3H bonds
  • Temp. where DNA strands half denatured are called melting temperature
  • Melting temp. varies according to each organisms DNA based on their G-C / A-T contents.
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15
Q

Describe the Renaturation of DNA double helix :

A
  • When the denatured DNA in solution is cooled down, complementary single strand DNA can reform into double stranded DNA with H bonding
  • Must be in presence of water
  • 37C
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16
Q

What are the significances of the denaturation and renaturation properties of DNA ?

A
  • Used in experiments such as Hybridization & Polymerase Chain Reaction (PCR)
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17
Q

Describe the steps of hybridisation & why it is performed :

A
  • Experiment performed to identify DNA homologous between two diff. organisms or their genes of interest.
    1. Heat to separate strands (Denaturation)
    2. Combine single strands of DNA
    3. Cool to allow renaturation of double stranded DNA (Renaturation)
    4. Determine degree of hybridization
18
Q

What are the 3 degrees of hybridization?

A

Complete hybridization : organisms identical

Partial hybridization : Organisms related

No hybridization : Organisms unrelated

19
Q

Describe what PCR does :

A
  • Uses denaturation & renaturation properties of DNA

- to help amplify target DNA sequences in large quantities

20
Q

Describe the typical structure of a 5’ to 3’ eukaryotic gene :

A
  • Promotor region
  • Transcription Initiation site
  • 5’ untranslated region (5’-UTR)
  • Translation start codon (ATG)
  • Exons (Coding)
  • Introns (Non-coding)
  • Translation stop codon
  • 3’ Untranslated Region (3’-UTR)
  • Transcription termination site
21
Q

What is the big difference between eukaryotic and prokaryotic gene structures?

A

Eukaryotic genes contain Introns.

Prokaryotic genes do not contain introns.

22
Q

How do eukaryotic mRNA differ from prokaryotic?

A
  • Eukaryotic mRNA is monocistronic. One mRNA is transcribed & translated into a protein.
  • Prokaryotic mRNA is polycistronic.
    One mRNA is transcribed & translated into multiple proteins.
23
Q

Recall the sections & percentages of the entire genome :

A

.

24
Q

What are Satellite or Tandem repeat sequences in the human genome?

A
  • Satellite DNA belong to non-coding tandem repeats DNA sequences
  • Repeated many times but always adjacent to each other
  • DNA repeat length ranges from 100 to 100,000 times
  • DNA repeat sequence size ranges from 1 to 300 bases
  • Due to being non-coding, satellite DNA mostly located in the heterochromatin region of the human genome i.e TELOMERES & CENTROMERES
25
Q

What is the difference between identical/perfect tandem repeats & degenerated/imperfect ones :

A
  • Identical tandem repeats have a 100% conserved unit sequences
  • Degenerated/imperfect tandem repeats have less than 100% unit sequence conserved
26
Q

What are the sizes of the different types of satellite DNAs ?

A
  • Micro-satellite : 1-9 bp
  • Mini-satellite : 10-100 bp
  • Macro-satellite : > 100 bp
27
Q

What are transposons?

A
  • Known as jumping genes since they can randomly move from one genomic location to another, in a process called transposition
  • 2 types : 1. DNA (3%) 2. RNA (retrotransposons) (41%)
28
Q

What are the two types of RNA transposons, and if applicable, their subdivisions?

A
  • Long terminal repeat transposons (LTR) 8%
  • Non-LTR transposons 33%, further divided into :
    1. Long interspersed nuclear elements (LINES) 20%
    2. Short interspersed nuclear elements (SINES) 13%
29
Q

How do Transposons move from one genomic location to another?

A
  • DNA transposons: simple cut & paste mechanism
  • RNA transposons (retrotransposons) :
    1. Copy themselves first into RNA via host RNA polymerase
    2. RNA will then be reverse transcribed into DNA by transposing encoded reverse transcriptase
    3. DNA inserted into another genomic location via transposons encoded integrase
30
Q

What triggers the transposons moving from one genomic location to another?

A
  • Environmental & genomic stresses seem to activate transpositions
31
Q

How does transposition affect the coding region of the genome?

A

Transposition occurring in :

  • Promotor region alters the gene expression
  • coding region disrupts its protein sequences
  • intron/exon boundaries disrupts its mRNA splicing
32
Q

Describe Alu elements (sequences) :

A
  • affects coding region
  • belongs to SINE retrotransposons
  • 300 bp long
  • over 1 million copies interspersed through human genome
  • Alu transpositions associated with various forms of cancer
33
Q

What is the percentage of genome containing no gene-related sequences and vice verse? What are the subdivisions ?

A
  • 60% contain no gene related sequences with 47% repetitive & 13% miscellaneous
  • 40% contain gene related sequences with 2% gene coding, 38% gene-related of which 26% are introns & 12% are unique regulatory & conserved sequences.
34
Q

What is the % of homology between the 2% of coding gene sequences of humans & chimpanzees?

A
  • 98% homology
35
Q

What is used during homology search?

A
  • Coding regions ONLY ( 2% in humans )
36
Q

What other sequences were used that could possibly differentiate human from chimp?

A
  • The 44% of ‘interspersed repetitive’ non-coding DNA sequences (transposons) of humans were compared to chimps
37
Q

What did the comparisons of the repetitive sequences of humans & chimps result in & suggest?

A
  • 4% of sequence differences were primarily identified in 41% of RNA transposons sequences
  • Suggests that retrotransposons might have played a role in human/chimp evolution/differentiation.
38
Q

What did further analysis of the repetitive sequences reveal ?

A
  • SINE retrotransposition rates remained similar between human, chimp & bonobo
  • LINE1 (subclass of LINEs) retrotransposition rates were LOWER in humans compared to chimps & bonobo
  • Thus suggests that LINE1 might have played a major role in human/chimp/bonobo evolution/differentiation from a common ancestor.
39
Q

What are the relations between Retrotranspositions & Species evolution ?

A
  • Retrotranspositions known to have capacity to move from one genomic location to another
  • High retrotransposition rates associated with changes in environment
  • Moving from one location to another & inducing mutations are considered as important drivers of human evolution
40
Q

What are the 3 conclusions of humans’ evolution from chimps and such?

A
  • Active mobilisation of retrotransposons occurred in the germ lines

+

  • Natural selection pressures ( physiological, environmental & cultural )

=

  • generation of genomic variation & phenotypic differences among these three species

Biochemistry (5 decks)

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